# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Sep 24 21:06:50 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 CZC  CZC  "[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate"  ligand  42  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CZC
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CZC  C1   C  CR6   0   0.665  44.9814  59.0759  -1.4030
 CZC  C2   C  CR56  0   0.639  43.6198  60.6160  -2.5749
 CZC  C3   C  CR56  0  -0.078  42.6252  60.5934  -1.6303
 CZC  C4   C  CH1   0   0.191  43.9181  61.8444  -4.7560
 CZC  C5   C  CH1   0  -0.013  43.4835  61.0200  -5.9786
 CZC  C6   C  CH1   0  -0.034  43.7602  62.0068  -7.1079
 CZC  C7   C  CH1   0  -0.055  43.3443  63.3261  -6.4482
 CZC  C8   C  CH2   0  -0.190  41.8819  63.6474  -6.6775
 CZC  C9   C  CR6   0   0.524  42.7629  59.7740  -0.4606
 CZC  C10  C  CR15  0   0.102  41.9871  61.9467  -3.1251
 CZC  N1   N  NR16  0  -0.735  43.9736  59.0776  -0.4631
 CZC  N2   N  NR16  0  -0.741  44.7622  59.8854  -2.4924
 CZC  N3   N  N     0  -0.432  41.6123  61.4374  -1.9954
 CZC  N4   N  NR5   0  -0.527  43.2217  61.4836  -3.5319
 CZC  O1   O  O     0  -0.461  45.9865  58.4106  -1.2803
 CZC  O2   O  OH1   0  -0.646  44.1745  59.8222  -6.1257
 CZC  O3   O  OH1   0  -0.659  45.1321  61.9665  -7.3871
 CZC  O4   O  O2    0  -0.483  43.6180  63.1712  -5.0544
 CZC  O5   O  O2    0  -0.578  41.5619  64.7960  -5.8855
 CZC  O6   O  O     0  -0.440  41.9743  59.6552   0.4543
 CZC  O7   O  O2    0  -0.699  40.4338  66.2376  -7.6504
 CZC  O8   O  OH1   0  -0.726  39.1139  64.6635  -6.2672
 CZC  O9   O  O     0  -0.667  40.1717  66.7817  -5.1188
 CZC  O10  O  OH1   0  -0.737  42.6427  67.4481  -7.2787
 CZC  O11  O  OH1   0  -0.724  40.5606  68.6861  -7.8268
 CZC  O12  O  O     0  -0.667  41.6491  67.1830  -9.6823
 CZC  P1   P  P     0   1.493  40.2932  65.7129  -6.1173
 CZC  P2   P  P     0   1.466  41.3843  67.4007  -8.2539
 CZC  H1   H  HCH1  0   0.268  44.9909  61.7131  -4.5713
 CZC  H2   H  HCH1  0   0.265  42.3992  60.8598  -5.9211
 CZC  H3   H  HCH1  0   0.263  43.1543  61.7878  -7.9964
 CZC  H4   H  HCH1  0   0.278  43.9478  64.1599  -6.8214
 CZC  H5   H  HCH2  0   0.266  41.7319  63.8461  -7.7420
 CZC  H6   H  HCH2  0   0.258  41.2316  62.8187  -6.3878
 CZC  H7   H  HCR5  0   0.302  41.4342  62.6678  -3.7057
 CZC  H8   H  HNR6  0   0.426  44.1420  58.4762   0.3341
 CZC  H9   H  HNR6  0   0.441  45.4665  59.8841  -3.2175
 CZC  H10  H  HOH1  0   0.466  43.7062  59.1308  -5.6478
 CZC  H11  H  HOH1  0   0.460  45.3241  62.6043  -8.0824
 CZC  H12  H  HOH1  0   0.509  38.2185  65.0313  -6.2447
 CZC  H13  H  HOH1  0   0.506  43.3679  66.8541  -7.5220
 CZC  H14  H  HOH1  0   0.507  40.8254  69.5029  -8.2737

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 CZC  O12  P2   double    1.469  0.020  1.469
 CZC  O11  P2   single    1.585  0.020  1.585
 CZC  P2   O10  single    1.593  0.020  1.593
 CZC  P2   O7   single    1.619  0.020  1.619
 CZC  O7   P1   single    1.627  0.020  1.627
 CZC  C6   O3   single    1.401  0.020  1.401
 CZC  C6   C5   single    1.525  0.020  1.525
 CZC  C6   C7   single    1.533  0.020  1.533
 CZC  O2   C5   single    1.391  0.020  1.391
 CZC  C8   C7   single    1.515  0.020  1.515
 CZC  C8   O5   single    1.431  0.020  1.431
 CZC  O9   P1   double    1.468  0.020  1.468
 CZC  P1   O5   single    1.582  0.020  1.582
 CZC  P1   O8   single    1.586  0.020  1.586
 CZC  C5   C4   single    1.537  0.020  1.537
 CZC  C7   O4   single    1.429  0.020  1.429
 CZC  C4   O4   single    1.393  0.020  1.393
 CZC  C4   N4   single    1.454  0.020  1.454
 CZC  N4   C10  aromatic  1.380  0.020  1.380
 CZC  N4   C2   aromatic  1.352  0.020  1.352
 CZC  C10  N3   aromatic  1.295  0.020  1.295
 CZC  C2   N2   single    1.359  0.020  1.359
 CZC  C2   C3   aromatic  1.372  0.020  1.372
 CZC  N2   C1   single    1.375  0.020  1.375
 CZC  N3   C3   aromatic  1.368  0.020  1.368
 CZC  C3   C9   single    1.435  0.020  1.435
 CZC  C1   O1   double    1.212  0.020  1.212
 CZC  C1   N1   single    1.378  0.020  1.378
 CZC  C9   N1   single    1.397  0.020  1.397
 CZC  C9   O6   double    1.214  0.020  1.214
 CZC  C4   H1   single    0.970  0.020  1.090
 CZC  C5   H2   single    0.970  0.020  1.090
 CZC  C6   H3   single    0.970  0.020  1.090
 CZC  C7   H4   single    0.970  0.020  1.090
 CZC  C8   H5   single    0.970  0.020  1.090
 CZC  C8   H6   single    0.970  0.020  1.090
 CZC  C10  H7   single    0.930  0.020  1.080
 CZC  N1   H8   single    0.860  0.020  1.020
 CZC  N2   H9   single    0.860  0.020  1.020
 CZC  O2   H10  single    0.850  0.020  0.980
 CZC  O3   H11  single    0.850  0.020  0.980
 CZC  O8   H12  single    0.850  0.020  0.980
 CZC  O10  H13  single    0.850  0.020  0.980
 CZC  O11  H14  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 CZC  O1   C1   N2   122.40  3.000
 CZC  O1   C1   N1   122.57  3.000
 CZC  N2   C1   N1   115.03  3.000
 CZC  N4   C2   N2   129.48  3.000
 CZC  N2   C2   C3   123.99  3.000
 CZC  N4   C2   C3   106.53  3.000
 CZC  N3   C3   C9   129.86  3.000
 CZC  C9   C3   C2   120.08  3.000
 CZC  N3   C3   C2   110.05  3.000
 CZC  H1   C4   O4   111.16  3.000
 CZC  H1   C4   N4   107.29  3.000
 CZC  O4   C4   N4   108.28  3.000
 CZC  H1   C4   C5   110.26  3.000
 CZC  N4   C4   C5   113.65  3.000
 CZC  O4   C4   C5   106.24  3.000
 CZC  H2   C5   O2   111.76  3.000
 CZC  H2   C5   C6   108.21  3.000
 CZC  O2   C5   C6   112.89  3.000
 CZC  H2   C5   C4   108.41  3.000
 CZC  O2   C5   C4   113.93  3.000
 CZC  C6   C5   C4   100.99  3.000
 CZC  H3   C6   O3   111.94  3.000
 CZC  H3   C6   C7   111.75  3.000
 CZC  O3   C6   C7   112.11  3.000
 CZC  H3   C6   C5   111.73  3.000
 CZC  C7   C6   C5   100.90  3.000
 CZC  O3   C6   C5   107.86  3.000
 CZC  H4   C7   O4   108.02  3.000
 CZC  H4   C7   C8   108.61  3.000
 CZC  O4   C7   C8   110.83  3.000
 CZC  H4   C7   C6   111.06  3.000
 CZC  O4   C7   C6   105.94  3.000
 CZC  C8   C7   C6   112.30  3.000
 CZC  H6   C8   H5   108.32  3.000
 CZC  H6   C8   O5   109.20  3.000
 CZC  H5   C8   O5   111.24  3.000
 CZC  H6   C8   C7   111.94  3.000
 CZC  H5   C8   C7   108.56  3.000
 CZC  O5   C8   C7   107.60  3.000
 CZC  O6   C9   N1   121.05  3.000
 CZC  O6   C9   C3   127.45  3.000
 CZC  N1   C9   C3   111.50  3.000
 CZC  H7   C10  N4   121.63  3.000
 CZC  H7   C10  N3   125.76  3.000
 CZC  N4   C10  N3   112.60  3.000
 CZC  H8   N1   C9   116.03  3.000
 CZC  H8   N1   C1   114.49  3.000
 CZC  C9   N1   C1   129.48  3.000
 CZC  H9   N2   C2   122.89  3.000
 CZC  H9   N2   C1   117.17  3.000
 CZC  C2   N2   C1   119.92  3.000
 CZC  C10  N3   C3   105.14  3.000
 CZC  C10  N4   C4   126.41  3.000
 CZC  C10  N4   C2   105.68  3.000
 CZC  C4   N4   C2   127.90  3.000
 CZC  H10  O2   C5   108.94  3.000
 CZC  H11  O3   C6   108.68  3.000
 CZC  C7   O4   C4   110.71  3.000
 CZC  P1   O5   C8   124.28  3.000
 CZC  P2   O7   P1   129.34  3.000
 CZC  H12  O8   P1   115.73  3.000
 CZC  H13  O10  P2   114.81  3.000
 CZC  H14  O11  P2   114.69  3.000
 CZC  O9   P1   O8   118.99  3.000
 CZC  O8   P1   O7   100.87  3.000
 CZC  O9   P1   O7   114.42  3.000
 CZC  O8   P1   O5   103.10  3.000
 CZC  O9   P1   O5   112.88  3.000
 CZC  O7   P1   O5   104.81  3.000
 CZC  O12  P2   O11  118.41  3.000
 CZC  O11  P2   O10  102.80  3.000
 CZC  O12  P2   O10  117.21  3.000
 CZC  O10  P2   O7   104.90  3.000
 CZC  O11  P2   O7   100.20  3.000
 CZC  O12  P2   O7   111.22  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 CZC  CONST_01  N3   C10  N4  C2     0.00   0.0  0
 CZC  CONST_02  C10  N3   C3  C2     0.00   0.0  0
 CZC  CONST_03  C10  N4   C2  C3     0.00   0.0  0
 CZC  CONST_04  N4   C10  N3  C3     0.00   0.0  0
 CZC  CONST_05  N4   C2   C3  N3     0.00   0.0  0
 CZC  CONST_06  C4   N4   C2  C3   180.00   0.0  0
 CZC  CONST_07  N3   C10  N4  C4   180.00   0.0  0
 CZC  CONST_08  N2   C2   N4  C4     0.00   0.0  0
 CZC  CONST_09  N1   C1   N2  C2     0.00   0.0  0
 CZC  CONST_10  N2   C1   N1  C9     0.00   0.0  0
 CZC  CONST_11  O1   C1   N2  C2   180.00   0.0  0
 CZC  CONST_12  O1   C1   N1  C9   180.00   0.0  0
 CZC  CONST_13  H7   C10  N4  C2   180.00   0.0  0
 CZC  CONST_14  H7   C10  N3  C3   180.00   0.0  0
 CZC  CONST_15  H7   C10  N4  C4     0.00   0.0  0
 CZC  CONST_16  H9   N2   C1  N1   180.00   0.0  0
 CZC  CONST_17  H8   N1   C1  N2   180.00   0.0  0
 CZC  CONST_18  H9   N2   C1  O1     0.00   0.0  0
 CZC  CONST_19  H8   N1   C1  O1     0.00   0.0  0
 CZC  Var_01    O6   C9   N1  C1   179.60  30.0  1
 CZC  Var_02    O6   C9   C3  C2   179.81  30.0  1
 CZC  Var_03    O6   C9   C3  N3     0.96  30.0  1
 CZC  Var_04    H8   N1   C9  O6     0.22  30.0  1
 CZC  Var_05    P1   O5   C8  C7   161.94  30.0  3
 CZC  Var_06    O7   P1   O5  C8   -57.78  30.0  1
 CZC  Var_07    O9   P1   O5  C8   177.07  30.0  1
 CZC  Var_08    O8   P1   O5  C8    47.40  30.0  1
 CZC  Var_09    P2   O7   P1  O5   -77.49  30.0  1
 CZC  Var_10    P2   O7   P1  O8   175.68  30.0  1
 CZC  Var_11    P2   O7   P1  O9    46.68  30.0  1
 CZC  Var_12    P1   O7   P2  O10   27.63  30.0  3
 CZC  Var_13    P1   O7   P2  O11  -78.67  30.0  3
 CZC  Var_14    P1   O7   P2  O12  155.28  30.0  3
 CZC  Var_15    H5   C8   O5  P1    43.15  30.0  1
 CZC  Var_16    H6   C8   O5  P1   -76.35  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CZC  chir_01  C4  C5  O4  N4  negativ
 CZC  chir_02  C5  O2  C6  C4  positiv
 CZC  chir_03  C6  O3  C7  C5  positiv
 CZC  chir_04  C7  O4  C6  C8  negativ
 CZC  chir_05  P1  O9  O5  O8  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CZC  plan-1  C3   0.020
 CZC  plan-1  C9   0.020
 CZC  plan-1  N1   0.020
 CZC  plan-1  O6   0.020
 CZC  plan-2  C1   0.020
 CZC  plan-2  C2   0.020
 CZC  plan-2  C3   0.020
 CZC  plan-2  C4   0.020
 CZC  plan-2  C9   0.020
 CZC  plan-2  C10  0.020
 CZC  plan-2  N1   0.020
 CZC  plan-2  N2   0.020
 CZC  plan-2  N3   0.020
 CZC  plan-2  N4   0.020
 CZC  plan-2  O1   0.020
 CZC  plan-2  H7   0.020
 CZC  plan-2  H8   0.020
 CZC  plan-2  H9   0.020

